rs7910620

Variant names:

• chr10-86087202-C-G
• rs7910620
• NM_017551.3:c.726+51617G>C

Your query was ambiguous. Multiple possible variants found:

• chr10-86087202-C-G
• chr10-86087202-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017551.3(GRID1):​c.726+51617G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0645 in 152,076 control chromosomes in the GnomAD database, including 783 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.065 (783 hom., cov: 32)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 7 publications found

Genes affected

GRID1 (HGNC:4575): (glutamate ionotropic receptor delta type subunit 1) This gene encodes a subunit of glutamate receptor channels. These channels mediate most of the fast excitatory synaptic transmission in the central nervous system and play key roles in synaptic plasticity.[provided by RefSeq, Jan 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRID1	NM_017551.3	c.726+51617G>C		intron_variant	Intron 4 of 15	ENST00000327946.12	NP_060021.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRID1	ENST00000327946.12	c.726+51617G>C		intron_variant	Intron 4 of 15	2	NM_017551.3	ENSP00000330148.7
GRID1	ENST00000464741.2	n.726+51617G>C		intron_variant	Intron 4 of 14	1		ENSP00000433064.1

Frequencies

GnomAD3 genomes AF: 0.0645 AC: 9798 AN: 151958 Hom.: 780 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0398

Gnomad ASJ AF: 0.00721

Gnomad EAS AF: 0.0590

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00798

Gnomad OTH AF: 0.0493

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0645 AC: 9813 AN: 152076 Hom.: 783 Cov.: 32 AF XY: 0.0638 AC XY: 4744 AN XY: 74350

African (AFR) AF: 0.185 AC: 7675 AN: 41444

American (AMR) AF: 0.0398 AC: 608 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00721 AC: 25 AN: 3468

East Asian (EAS) AF: 0.0584 AC: 302 AN: 5172

South Asian (SAS) AF: 0.108 AC: 518 AN: 4796

European-Finnish (FIN) AF: 0.000189 AC: 2 AN: 10594

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00799 AC: 543 AN: 68002

Other (OTH) AF: 0.0483 AC: 102 AN: 2110

Alfa AF: 0.0102 Hom.: 16

Bravo AF: 0.0719

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.2
DANN	Benign	0.53
PhyloP100		0.53
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7910620; hg19: chr10-87846959;